Calcium in PDB 7pc5: The Third Pdz Domain of PDZD7 Complexed with the Pdz-Binding Motif of EXOC4

Protein crystallography data

The structure of The Third Pdz Domain of PDZD7 Complexed with the Pdz-Binding Motif of EXOC4, PDB code: 7pc5 was solved by A.Cousido-Siah, G.Trave, G.Gogl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.75 / 1.70
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.11, 60.35, 181.68, 90, 90, 90
R / Rfree (%) 16.6 / 18.8

Calcium Binding Sites:

The binding sites of Calcium atom in the The Third Pdz Domain of PDZD7 Complexed with the Pdz-Binding Motif of EXOC4 (pdb code 7pc5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the The Third Pdz Domain of PDZD7 Complexed with the Pdz-Binding Motif of EXOC4, PDB code: 7pc5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 7pc5

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Calcium binding site 1 out of 5 in the The Third Pdz Domain of PDZD7 Complexed with the Pdz-Binding Motif of EXOC4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Third Pdz Domain of PDZD7 Complexed with the Pdz-Binding Motif of EXOC4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1301

b:58.6
occ:1.00
 OE1 A:GLU986 2.4 47.6 1.0
O A:VAL984 2.5 36.9 1.0
O A:GLY983 2.6 39.4 1.0
OE2 A:GLU986 2.7 38.9 1.0
CD A:GLU986 2.9 41.8 1.0
C A:GLY983 3.5 39.9 1.0
C A:VAL984 3.7 29.5 1.0
N A:VAL984 4.2 33.3 1.0
O A:HOH1497 4.3 44.0 1.0
CA A:VAL984 4.3 29.3 1.0
CB A:VAL984 4.4 29.5 1.0
CG A:GLU986 4.4 28.4 1.0
CA A:GLY983 4.4 41.9 1.0
O A:HOH1728 4.6 45.4 1.0
N A:GLU986 4.7 25.9 1.0
N A:ASP985 4.8 27.7 1.0

Calcium binding site 2 out of 5 in 7pc5

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Calcium binding site 2 out of 5 in the The Third Pdz Domain of PDZD7 Complexed with the Pdz-Binding Motif of EXOC4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Third Pdz Domain of PDZD7 Complexed with the Pdz-Binding Motif of EXOC4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1302

b:64.1
occ:1.00
 O A:HOH1733 2.2 58.7 1.0
O A:HOH1698 2.2 50.3 1.0
O A:LYS1021 2.5 35.5 1.0
O A:LEU1024 2.7 29.5 1.0
OE1 A:GLU1029 2.7 39.8 1.0
CD A:GLU1029 3.4 41.6 1.0
OE2 A:GLU1029 3.6 45.6 1.0
C A:LYS1021 3.7 35.6 1.0
C A:LEU1024 3.8 29.1 1.0
CA A:SER1025 4.3 28.7 1.0
CG A:LYS1021 4.5 41.2 1.0
CA A:SER1022 4.5 30.3 1.0
O A:SER1022 4.5 37.1 1.0
CA A:LYS1021 4.6 33.0 1.0
N A:SER1025 4.6 26.7 1.0
N A:SER1022 4.6 29.0 1.0
CB A:SER1025 4.6 35.2 1.0
CG A:GLU1029 4.6 27.8 1.0
C A:SER1022 4.6 37.2 1.0
N A:LEU1024 4.8 25.9 1.0
CA A:LEU1024 4.9 25.8 1.0

Calcium binding site 3 out of 5 in 7pc5

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Calcium binding site 3 out of 5 in the The Third Pdz Domain of PDZD7 Complexed with the Pdz-Binding Motif of EXOC4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Third Pdz Domain of PDZD7 Complexed with the Pdz-Binding Motif of EXOC4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1303

b:50.9
occ:1.00
 O A:MET1051 2.6 37.1 1.0
O A:GLY1055 2.7 34.0 1.0
OD1 A:ASP1095 2.7 64.1 1.0
O A:GLY1053 2.7 34.5 1.0
O A:HOH1442 3.0 42.2 1.0
O A:HOH1751 3.3 61.5 1.0
C A:MET1051 3.5 32.7 1.0
CG A:ASP1095 3.5 48.5 1.0
OD2 A:ASP1095 3.5 51.3 1.0
C A:GLY1055 3.5 46.8 1.0
C A:GLY1053 3.8 35.9 1.0
N A:GLY1055 3.8 41.9 1.0
O A:LYS1052 4.1 37.6 1.0
C A:LYS1052 4.1 37.7 1.0
CA A:GLY1055 4.1 41.4 1.0
O A:HOH1597 4.1 44.2 1.0
CA A:MET1051 4.2 24.9 1.0
N A:LYS1052 4.2 32.0 1.0
N A:GLY1053 4.3 34.4 1.0
OG1 A:THR1056 4.3 44.2 1.0
C A:LEU1054 4.3 44.6 1.0
CA A:LYS1052 4.5 35.8 1.0
N A:THR1056 4.5 38.2 1.0
CA A:GLY1053 4.7 32.4 1.0
N A:LEU1054 4.7 29.3 1.0
CA A:LEU1054 4.7 28.5 1.0
CA A:THR1056 4.8 31.7 1.0
CB A:MET1051 4.9 29.3 1.0
O A:LEU1054 4.9 44.0 1.0
CB A:ASP1095 4.9 33.1 1.0

Calcium binding site 4 out of 5 in 7pc5

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Calcium binding site 4 out of 5 in the The Third Pdz Domain of PDZD7 Complexed with the Pdz-Binding Motif of EXOC4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Third Pdz Domain of PDZD7 Complexed with the Pdz-Binding Motif of EXOC4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1304

b:32.7
occ:1.00
 O A:GLY1140 2.3 29.4 1.0
O A:ARG1138 2.3 29.4 1.0
O A:GLY1135 2.3 29.4 1.0
OE1 A:GLU1180 2.4 26.4 1.0
O A:HOH1662 2.5 42.7 1.0
O A:HOH1747 2.5 38.0 1.0
OE2 A:GLU1180 2.6 30.9 1.0
CD A:GLU1180 2.8 31.2 1.0
C A:GLY1135 3.3 30.9 1.0
C A:GLY1140 3.4 34.7 1.0
C A:ARG1138 3.5 34.7 1.0
N A:GLY1140 3.7 39.5 1.0
CA A:GLY1140 4.0 38.0 1.0
CA A:GLY1135 4.1 26.2 1.0
C A:LYS1139 4.1 36.6 1.0
CA A:VAL1136 4.1 27.0 0.3
N A:VAL1136 4.1 27.2 0.3
N A:VAL1136 4.2 26.0 0.7
OG1 A:THR1141 4.2 31.5 1.0
CA A:VAL1136 4.2 25.9 0.7
N A:ARG1138 4.3 37.8 1.0
CG A:ARG1138 4.4 26.9 1.0
CG A:GLU1180 4.4 27.2 1.0
O A:HOH1523 4.4 36.0 1.0
CA A:LYS1139 4.4 35.6 1.0
N A:LYS1139 4.4 34.2 1.0
C A:VAL1136 4.4 32.0 0.7
CA A:ARG1138 4.4 37.4 1.0
N A:THR1141 4.4 29.6 1.0
O A:VAL1136 4.5 31.2 0.7
C A:VAL1136 4.5 30.6 0.3
O A:HOH1744 4.6 47.3 1.0
O A:LYS1139 4.7 38.4 1.0
CA A:THR1141 4.8 26.4 1.0
O A:HOH1583 4.8 44.0 1.0
O A:VAL1136 4.9 30.9 0.3

Calcium binding site 5 out of 5 in 7pc5

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Calcium binding site 5 out of 5 in the The Third Pdz Domain of PDZD7 Complexed with the Pdz-Binding Motif of EXOC4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Third Pdz Domain of PDZD7 Complexed with the Pdz-Binding Motif of EXOC4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1305

b:20.1
occ:1.00
 O A:GLY1213 2.4 21.8 1.0
O A:GLY1215 2.4 23.8 1.0
O A:MET1211 2.4 20.1 1.0
OD1 A:ASP1255 2.5 20.5 1.0
OD2 A:ASP1255 2.5 21.4 1.0
CG A:ASP1255 2.8 23.4 1.0
C A:MET1211 3.4 19.0 1.0
C A:GLY1215 3.5 26.2 1.0
C A:GLY1213 3.6 24.3 1.0
N A:GLY1215 4.0 25.2 1.0
CA A:MET1211 4.0 16.7 1.0
N A:GLY1213 4.1 23.3 1.0
CA A:GLY1215 4.2 29.1 1.0
C A:LYS1214 4.2 25.6 1.0
C A:LYS1212 4.3 20.8 1.0
CB A:ASP1255 4.3 21.4 1.0
O A:HOH1647 4.3 30.6 1.0
OG1 A:THR1216 4.4 24.8 1.0
CA A:GLY1213 4.4 23.6 1.0
N A:LYS1212 4.5 20.4 1.0
N A:THR1216 4.5 21.1 1.0
N A:LYS1214 4.6 23.6 1.0
CB A:MET1211 4.6 19.4 1.0
O A:LYS1214 4.7 26.1 1.0
O A:LYS1212 4.7 23.6 1.0
CA A:LYS1214 4.7 23.8 1.0
CA A:THR1216 4.8 22.6 1.0
O A:HOH1556 4.8 20.9 1.0
CA A:LYS1212 4.9 19.7 1.0
CA A:ASP1255 5.0 21.4 1.0
O A:HOH1614 5.0 33.4 1.0

Reference:

A.Cousido-Siah, L.Carneiro, C.Kostmann, P.Ecsedi, L.Nyitray, G.Trave, G.Gogl. A Scalable Strategy to Solve Structures of Pdz Domains and Their Complexes. Acta Crystallogr D Struct V. 78 509 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35362473
DOI: 10.1107/S2059798322001784
Page generated: Fri Jul 19 02:50:45 2024

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